DICOMAnalyzer / app.py
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Update app.py
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import gradio as gr
import cv2
import numpy as np
import pandas as pd
import pydicom
import io
from PIL import Image
import openpyxl
from openpyxl.utils import get_column_letter, column_index_from_string
import logging
import time
import traceback
from functools import wraps
import sys
print("Starting imports completed...")
# Set up logging
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s',
handlers=[
logging.FileHandler('dicom_analyzer_debug.log'),
logging.StreamHandler(sys.stdout)
]
)
logger = logging.getLogger(__name__)
def debug_decorator(func):
@wraps(func)
def wrapper(*args, **kwargs):
logger.debug(f"Entering {func.__name__}")
start_time = time.time()
try:
result = func(*args, **kwargs)
logger.debug(f"Function {func.__name__} completed successfully")
return result
except Exception as e:
logger.error(f"Error in {func.__name__}: {str(e)}")
logger.error(traceback.format_exc())
raise
finally:
end_time = time.time()
logger.debug(f"Execution time: {end_time - start_time:.4f} seconds")
return wrapper
class DicomAnalyzer:
def __init__(self):
self.results = []
self.circle_diameter = 9.0
self.zoom_factor = 1.0
self.current_image = None
self.dicom_data = None
self.display_image = None
self.marks = []
self.original_image = None
self.original_display = None
self.pan_x = 0
self.pan_y = 0
self.max_pan_x = 0
self.max_pan_y = 0
self.CIRCLE_COLOR = (0, 255, 255) # BGR format
self.SMALL_CIRCLES_COLOR = (255, 255, 255) # BGR white
print("DicomAnalyzer initialized...")
def save_results(self):
try:
if not self.results:
logger.warning("Attempted to save with no results")
return None, "No results to save"
df = pd.DataFrame(self.results)
columns_order = ['Area (mm²)', 'Mean', 'StdDev', 'Min', 'Max', 'Point']
df = df[columns_order]
timestamp = time.strftime("%Y%m%d_%H%M%S")
output_file = f"analysis_results_{timestamp}.xlsx"
with pd.ExcelWriter(output_file, engine='openpyxl') as writer:
df.to_excel(writer, index=False, sheet_name='Results')
worksheet = writer.sheets['Results']
for idx, col in enumerate(df.columns):
max_length = max(
df[col].astype(str).apply(len).max(),
len(str(col))
) + 2
worksheet.column_dimensions[get_column_letter(idx + 1)].width = max_length
logger.info(f"Results saved successfully to {output_file}")
return output_file, f"Results saved successfully to {output_file}"
except Exception as e:
error_msg = f"Error saving results: {str(e)}"
logger.error(error_msg)
logger.error(traceback.format_exc())
return None, error_msg
def reset_all(self, image):
self.results = []
self.marks = []
self.reset_view()
return self.update_display(), "All data has been reset"
def load_dicom(self, file):
try:
if file is None:
return None, "No file uploaded"
if hasattr(file, 'name'):
dicom_data = pydicom.dcmread(file.name)
else:
dicom_data = pydicom.dcmread(file)
image = dicom_data.pixel_array.astype(np.float32)
self.original_image = image.copy()
rescale_slope = getattr(dicom_data, 'RescaleSlope', 1)
rescale_intercept = getattr(dicom_data, 'RescaleIntercept', 0)
image = (image * rescale_slope) + rescale_intercept
self.current_image = image
self.dicom_data = dicom_data
self.display_image = self.normalize_image(image)
self.original_display = self.display_image.copy()
self.reset_all(None)
print("DICOM file loaded successfully")
return self.display_image, "DICOM file loaded successfully"
except Exception as e:
print(f"Error loading DICOM file: {str(e)}")
return None, f"Error loading DICOM file: {str(e)}"
def normalize_image(self, image):
try:
normalized = cv2.normalize(
image,
None,
alpha=0,
beta=255,
norm_type=cv2.NORM_MINMAX,
dtype=cv2.CV_8U
)
if len(normalized.shape) == 2:
normalized = cv2.cvtColor(normalized, cv2.COLOR_GRAY2BGR)
return normalized
except Exception as e:
print(f"Error normalizing image: {str(e)}")
return None
def reset_view(self):
self.zoom_factor = 1.0
self.pan_x = 0
self.pan_y = 0
if self.original_display is not None:
return self.update_display()
return None
def zoom_in(self, image):
print("Zooming in...")
self.zoom_factor = min(20.0, self.zoom_factor + 0.5)
return self.update_display()
def zoom_out(self, image):
print("Zooming out...")
self.zoom_factor = max(1.0, self.zoom_factor - 0.5)
return self.update_display()
def handle_keyboard(self, key):
try:
print(f"Handling key press: {key}")
pan_amount = int(10 * self.zoom_factor)
if key == 'ArrowLeft':
self.pan_x = max(0, self.pan_x - pan_amount)
elif key == 'ArrowRight':
self.pan_x = min(self.max_pan_x, self.pan_x + pan_amount)
elif key == 'ArrowUp':
self.pan_y = max(0, self.pan_y - pan_amount)
elif key == 'ArrowDown':
self.pan_y = min(self.max_pan_y, self.pan_y + pan_amount)
return self.update_display()
except Exception as e:
print(f"Error handling keyboard input: {str(e)}")
return self.display_image
def update_display(self):
try:
if self.original_display is None:
return None
height, width = self.original_display.shape[:2]
new_height = int(height * self.zoom_factor)
new_width = int(width * self.zoom_factor)
zoomed = cv2.resize(
self.original_display,
(new_width, new_height),
interpolation=cv2.INTER_CUBIC
)
zoomed_bgr = cv2.cvtColor(zoomed, cv2.COLOR_RGB2BGR)
for x, y, diameter in self.marks:
zoomed_x = int(x * self.zoom_factor)
zoomed_y = int(y * self.zoom_factor)
zoomed_radius = int((diameter / 2.0) * self.zoom_factor)
# Draw the main yellow circle
cv2.circle(
zoomed_bgr,
(zoomed_x, zoomed_y),
zoomed_radius,
self.CIRCLE_COLOR,
1,
lineType=cv2.LINE_AA
)
# Draw 8 small white circles around
num_points = 8
for i in range(num_points):
angle = 2 * np.pi * i / num_points
point_x = int(zoomed_x + zoomed_radius * np.cos(angle))
point_y = int(zoomed_y + zoomed_radius * np.sin(angle))
cv2.circle(
zoomed_bgr,
(point_x, point_y),
1,
self.SMALL_CIRCLES_COLOR,
-1,
lineType=cv2.LINE_AA
)
zoomed = cv2.cvtColor(zoomed_bgr, cv2.COLOR_BGR2RGB)
self.max_pan_x = max(0, new_width - width)
self.max_pan_y = max(0, new_height - height)
self.pan_x = min(max(0, self.pan_x), self.max_pan_x)
self.pan_y = min(max(0, self.pan_y), self.max_pan_y)
visible = zoomed[
int(self.pan_y):int(self.pan_y + height),
int(self.pan_x):int(self.pan_x + width)
]
return visible
except Exception as e:
print(f"Error updating display: {str(e)}")
return self.original_display
def analyze_roi(self, evt: gr.SelectData):
try:
if self.current_image is None:
return None, "No image loaded"
clicked_x = evt.index[0]
clicked_y = evt.index[1]
x = clicked_x + self.pan_x
y = clicked_y + self.pan_y
if self.zoom_factor != 1.0:
x = x / self.zoom_factor
y = y / self.zoom_factor
x = int(round(x))
y = int(round(y))
height, width = self.original_image.shape[:2]
Y, X = np.ogrid[:height, :width]
radius = self.circle_diameter / 2.0
r_squared = radius * radius
dx = X - x
dy = Y - y
dist_squared = dx * dx + dy * dy
mask = np.zeros((height, width), dtype=bool)
mask[dist_squared <= r_squared] = True
roi_pixels = self.original_image[mask]
if len(roi_pixels) == 0:
return self.display_image, "Error: No pixels selected"
pixel_spacing = float(self.dicom_data.PixelSpacing[0])
n_pixels = np.sum(mask)
area = n_pixels * (pixel_spacing ** 2)
mean_value = np.mean(roi_pixels)
std_dev = np.std(roi_pixels, ddof=1)
min_val = np.min(roi_pixels)
max_val = np.max(roi_pixels)
rescale_slope = getattr(self.dicom_data, 'RescaleSlope', 1)
rescale_intercept = getattr(self.dicom_data, 'RescaleIntercept', 0)
mean_value = (mean_value * rescale_slope) + rescale_intercept
std_dev = std_dev * rescale_slope
min_val = (min_val * rescale_slope) + rescale_intercept
max_val = (max_val * rescale_slope) + rescale_intercept
result = {
'Area (mm²)': f"{area:.3f}",
'Mean': f"{mean_value:.3f}",
'StdDev': f"{std_dev:.3f}",
'Min': f"{min_val:.3f}",
'Max': f"{max_val:.3f}",
'Point': f"({x}, {y})"
}
self.results.append(result)
self.marks.append((x, y, self.circle_diameter))
return self.update_display(), self.format_results()
except Exception as e:
print(f"Error analyzing ROI: {str(e)}")
return self.display_image, f"Error analyzing ROI: {str(e)}"
def add_formulas_to_template(self, ws, row_pair, col_group, red_font):
"""
Inserts SNR (first row) and CNR (second row) formulas with IFERROR.
"""
try:
base_col = col_group[1] # Mean column
std_col = col_group[2] # StdDev column
row1, row2 = row_pair
# SNR formula
formula1 = f"=IFERROR({base_col}{row1}/{std_col}{row1},\"\")"
formula_col = get_column_letter(column_index_from_string(col_group[-1]) + 1)
cell1 = ws[f"{formula_col}{row1}"]
cell1.value = formula1
cell1.font = red_font
cell1.alignment = openpyxl.styles.Alignment(horizontal='center')
# CNR formula
formula2 = f"=IFERROR(({base_col}{row1}-{base_col}{row2})/{std_col}{row2},\"\")"
cell2 = ws[f"{formula_col}{row2}"]
cell2.value = formula2
cell2.font = red_font
cell2.alignment = openpyxl.styles.Alignment(horizontal='center')
logger.debug(f"Added formulas for rows {row1},{row2} in column {formula_col}")
except Exception as e:
logger.error(f"Error adding formulas: {str(e)}")
def save_formatted_results(self, output_path):
try:
if not self.results:
return None, "No results to save"
wb = openpyxl.Workbook()
ws = wb.active
red_font = openpyxl.styles.Font(color="FF0000")
center_alignment = openpyxl.styles.Alignment(horizontal='center')
headers = ['Area', 'Mean', 'StdDev', 'Min', 'Max']
column_groups = [
('B', 'C', 'D', 'E', 'F'), ('H', 'I', 'J', 'K', 'L'),
('N', 'O', 'P', 'Q', 'R'), ('T', 'U', 'V', 'W', 'X'),
('Z', 'AA', 'AB', 'AC', 'AD'), ('AF', 'AG', 'AH', 'AI', 'AJ'),
('AL', 'AM', 'AN', 'AO', 'AP'), ('AR', 'AS', 'AT', 'AU', 'AV'),
('AX', 'AY', 'AZ', 'BA', 'BB'), ('BD', 'BE', 'BF', 'BG', 'BH'),
('BJ', 'BK', 'BL', 'BM', 'BN'), ('BP', 'BQ', 'BR', 'BS', 'BT'),
('BV', 'BW', 'BX', 'BY', 'BZ')
]
for cols in column_groups:
for i, header in enumerate(headers):
cell = ws[f"{cols[i]}1"]
cell.value = header
cell.alignment = center_alignment
row_pairs = [
(2, 3), (5, 6), (8, 9), (11, 12), (14, 15),
(17, 18), (20, 21), (23, 24), (26, 27), (29, 30)
]
phantom_sizes = [
'(7mm)', '(6.5mm)', '(6mm)', '(5.5mm)', '(5mm)',
'(4.5mm)', '(4mm)', '(3.5mm)', '(3mm)', '(2.5mm)'
]
for i, size in enumerate(phantom_sizes):
header_cell = ws.cell(row=row_pairs[i][0]-1, column=1, value=size)
header_cell.font = red_font
header_cell.alignment = center_alignment
result_idx = 0
current_col_group = 0
current_row_pair = 0
while result_idx < len(self.results):
if current_row_pair >= len(row_pairs):
break
cols = column_groups[current_col_group]
rows = row_pairs[current_row_pair]
if result_idx < len(self.results):
result = self.results[result_idx]
self._write_result_to_cells(ws, result, cols, rows[0])
result_idx += 1
if result_idx < len(self.results):
result = self.results[result_idx]
self._write_result_to_cells(ws, result, cols, rows[1])
result_idx += 1
self.add_formulas_to_template(ws, rows, cols, red_font)
current_col_group += 1
if current_col_group >= len(column_groups):
current_col_group = 0
current_row_pair += 1
for cols in column_groups:
for col in cols:
for row in range(2, 31):
cell = ws[f"{col}{row}"]
if cell.value is not None:
cell.alignment = center_alignment
# StdDev Averages
current_row = 32
stddev_header = ws.cell(row=current_row, column=1, value="StdDev Averages")
stddev_header.font = red_font
stddev_header.alignment = center_alignment
current_row += 1
for i, size in enumerate(phantom_sizes):
row_number = row_pairs[i][0]
stddev_values = []
for cols in column_groups:
stddev_col = cols[2]
cell_value = ws[f"{stddev_col}{row_number}"].value
if cell_value not in [0, None, '']:
stddev_values.append(float(cell_value))
size_cell = ws.cell(row=current_row, column=1, value=size)
size_cell.alignment = center_alignment
if stddev_values:
avg_stddev = sum(stddev_values) / len(stddev_values)
avg_cell = ws.cell(row=current_row, column=2, value=avg_stddev)
avg_cell.number_format = '0.000'
avg_cell.alignment = center_alignment
current_row += 1
# Mean Averages
current_row += 2
mean_header = ws.cell(row=current_row, column=1, value="Mean Averages")
mean_header.font = red_font
mean_header.alignment = center_alignment
current_row += 1
for i, size in enumerate(phantom_sizes):
row_number = row_pairs[i][0] # نأخذ الصف الأول فقط
mean_values = []
for cols in column_groups:
mean_col = cols[1] # The Mean column
cell_value = ws[f"{mean_col}{row_number}"].value
if cell_value not in [0, None, '']:
mean_values.append(float(cell_value))
size_cell = ws.cell(row=current_row, column=1, value=size)
size_cell.alignment = center_alignment
if mean_values:
avg_mean = sum(mean_values) / len(mean_values)
avg_cell = ws.cell(row=current_row, column=2, value=avg_mean)
avg_cell.number_format = '0.000'
avg_cell.alignment = center_alignment
current_row += 1
current_row += 2
# CNR Averages
cnr_header = ws.cell(row=current_row, column=1, value="CNR Averages")
cnr_header.font = red_font
cnr_header.alignment = center_alignment
current_row += 1
for i, size in enumerate(phantom_sizes):
row_number = row_pairs[i][1]
cnr_cells = []
for cols in column_groups:
formula_col = get_column_letter(column_index_from_string(cols[-1]) + 1)
cnr_cell_ref = f"{formula_col}{row_number}"
mean_col = cols[1]
std_col = cols[2]
mean1_val = ws[f"{mean_col}{row_pairs[i][0]}"].value
mean2_val = ws[f"{mean_col}{row_pairs[i][1]}"].value
std2_val = ws[f"{std_col}{row_pairs[i][1]}"].value
try:
mean1_val = float(mean1_val) if mean1_val not in [None, ''] else 0
mean2_val = float(mean2_val) if mean2_val not in [None, ''] else 0
std2_val = float(std2_val) if std2_val not in [None, ''] else 0
except:
mean1_val, mean2_val, std2_val = 0, 0, 0
if not (mean1_val == 0 and mean2_val == 0 and std2_val == 0):
cnr_cells.append(cnr_cell_ref)
size_cell = ws.cell(row=current_row, column=1, value=size)
size_cell.alignment = center_alignment
if cnr_cells:
average_formula = f'=IFERROR(AVERAGE({",".join(cnr_cells)}), "")'
avg_cell = ws.cell(row=current_row, column=2)
avg_cell.value = average_formula
avg_cell.number_format = '0.000'
avg_cell.alignment = center_alignment
current_row += 1
for row in range(32, current_row):
for col in range(1, 3):
cell = ws.cell(row=row, column=col)
cell.alignment = center_alignment
wb.save(output_path)
return output_path, f"Results saved successfully ({len(self.results)} measurements)"
except Exception as e:
logger.error(f"Error saving formatted results: {str(e)}")
return None, f"Error saving results: {str(e)}"
def _write_result_to_cells(self, ws, result, cols, row):
center_alignment = openpyxl.styles.Alignment(horizontal='center')
value_mapping = {
'Area': 'Area (mm²)',
'Mean': 'Mean',
'StdDev': 'StdDev',
'Min': 'Min',
'Max': 'Max'
}
for i, (header, key) in enumerate(value_mapping.items()):
cell = ws[f"{cols[i]}{row}"]
val = result[key]
cell.value = float(val) if val not in ['', None] else ''
cell.alignment = center_alignment
def format_results(self):
if not self.results:
return "No measurements yet"
df = pd.DataFrame(self.results)
columns_order = ['Area (mm²)', 'Mean', 'StdDev', 'Min', 'Max', 'Point']
df = df[columns_order]
return df.to_string(index=False)
def add_zero_row(self, image):
self.results.append({
'Area (mm²)': '0.000',
'Mean': '0.000',
'StdDev': '0.000',
'Min': '0.000',
'Max': '0.000',
'Point': '(0, 0)'
})
return image, self.format_results()
def add_two_zero_rows(self, image):
for _ in range(2):
self.results.append({
'Area (mm²)': '0.000',
'Mean': '0.000',
'StdDev': '0.000',
'Min': '0.000',
'Max': '0.000',
'Point': '(0, 0)'
})
return image, self.format_results()
def undo_last(self, image):
if not self.results: # لو مفيش نتائج أصلاً
return self.update_display(), self.format_results()
last_result = self.results[-1]
# نتحقق إذا كان آخر إجراء قياس حقيقي أم صف صفري
is_measurement = last_result['Point'] != '(0, 0)'
# نمسح آخر نتيجة
self.results.pop()
# لو كان قياس حقيقي، نمسح العلامة المقابلة له
if is_measurement and self.marks:
self.marks.pop()
return self.update_display(), self.format_results()
def create_interface():
print("Creating interface...")
analyzer = DicomAnalyzer()
with gr.Blocks(css="#image_display { outline: none; }") as interface:
gr.Markdown("# DICOM Image Analyzer")
with gr.Row():
with gr.Column():
file_input = gr.File(label="Upload DICOM file")
diameter_slider = gr.Slider(
minimum=1,
maximum=20,
value=9,
step=1,
label="ROI Diameter (pixels)"
)
with gr.Row():
zoom_in_btn = gr.Button("Zoom In (+)")
zoom_out_btn = gr.Button("Zoom Out (-)")
reset_btn = gr.Button("Reset View")
reset_all_btn = gr.Button("Reset All")
with gr.Column():
image_display = gr.Image(
label="DICOM Image",
interactive=True,
elem_id="image_display"
)
with gr.Row():
zero_btn = gr.Button("Add Zero Row")
zero2_btn = gr.Button("Add Two Zero Rows")
undo_btn = gr.Button("Undo Last")
save_btn = gr.Button("Save Results")
save_formatted_btn = gr.Button("Save Formatted Results")
results_display = gr.Textbox(label="Results", interactive=False)
file_output = gr.File(label="Download Results")
key_press = gr.Textbox(visible=False, elem_id="key_press")
gr.Markdown("""
### Controls:
- Use arrow keys to pan when zoomed in. Movement is now larger.
- Click points to measure ROI.
- Use Zoom In/Out buttons or Reset View to adjust zoom level.
- Use Reset All to clear all measurements.
- "Save Results": basic Excel with raw data.
- "Save Formatted Results": Excel with advanced formatting & formulas.
""")
def update_diameter(x):
analyzer.circle_diameter = float(x)
print(f"Diameter updated to: {x}")
return f"Diameter set to {x} pixels"
def save_formatted():
output_path = "analysis_results_formatted.xlsx"
return analyzer.save_formatted_results(output_path)
file_input.change(
fn=analyzer.load_dicom,
inputs=file_input,
outputs=[image_display, results_display]
)
image_display.select(
fn=analyzer.analyze_roi,
outputs=[image_display, results_display]
)
diameter_slider.change(
fn=update_diameter,
inputs=diameter_slider,
outputs=gr.Textbox(label="Status")
)
zoom_in_btn.click(
fn=analyzer.zoom_in,
inputs=image_display,
outputs=image_display,
queue=False
)
zoom_out_btn.click(
fn=analyzer.zoom_out,
inputs=image_display,
outputs=image_display,
queue=False
)
reset_btn.click(
fn=analyzer.reset_view,
outputs=image_display
)
reset_all_btn.click(
fn=analyzer.reset_all,
inputs=image_display,
outputs=[image_display, results_display]
)
key_press.change(
fn=analyzer.handle_keyboard,
inputs=key_press,
outputs=image_display
)
zero_btn.click(
fn=analyzer.add_zero_row,
inputs=image_display,
outputs=[image_display, results_display]
)
zero2_btn.click(
fn=analyzer.add_two_zero_rows,
inputs=image_display,
outputs=[image_display, results_display]
)
undo_btn.click(
fn=analyzer.undo_last,
inputs=image_display,
outputs=[image_display, results_display]
)
save_btn.click(
fn=analyzer.save_results,
outputs=[file_output, results_display]
)
save_formatted_btn.click(
fn=save_formatted,
outputs=[file_output, results_display]
)
js = """
<script>
document.addEventListener('keydown', function(e) {
if (['ArrowUp', 'ArrowDown', 'ArrowLeft', 'ArrowRight'].includes(e.key)) {
e.preventDefault();
const keyPressElement = document.querySelector('#key_press textarea');
if (keyPressElement) {
keyPressElement.value = e.key;
keyPressElement.dispatchEvent(new Event('input'));
setTimeout(() => {
keyPressElement.value = '';
keyPressElement.dispatchEvent(new Event('input'));
}, 100);
}
}
});
</script>
"""
gr.HTML(js)
print("Interface created successfully")
return interface
if __name__ == "__main__":
try:
print("Starting application...")
interface = create_interface()
print("Launching interface...")
interface.queue()
interface.launch(
server_name="0.0.0.0",
server_port=7860,
share=True,
debug=True,
show_error=True,
quiet=False
)
except Exception as e:
print(f"Error launching application: {str(e)}")
logger.error(f"Error launching application: {str(e)}")
logger.error(traceback.format_exc())
raise e